12-119690180-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001206999.2(CIT):c.6157G>A(p.Val2053Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000922 in 1,486,374 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001206999.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152178Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000977 AC: 14AN: 143286Hom.: 0 AF XY: 0.0000886 AC XY: 7AN XY: 78998
GnomAD4 exome AF: 0.0000944 AC: 126AN: 1334078Hom.: 1 Cov.: 31 AF XY: 0.0000903 AC XY: 59AN XY: 653306
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152296Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 4AN XY: 74468
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.6157G>A (p.V2053M) alteration is located in exon 47 (coding exon 46) of the CIT gene. This alteration results from a G to A substitution at nucleotide position 6157, causing the valine (V) at amino acid position 2053 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 2053 of the CIT protein (p.Val2053Met). This variant is present in population databases (rs764137343, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with CIT-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at